data_2DJH # _model_server_result.job_id K8kPHGFsvuWMGYowqkhHtw _model_server_result.datetime_utc '2024-10-19 16:23:45' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 2djh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":117}' # _entry.id 2DJH # _exptl.entry_id 2DJH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-AMINO-9-(2-DEOXY-3-O-PHOSPHONOPENTOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 2DJH _cell.length_a 29.19 _cell.length_b 48.72 _cell.length_c 62.58 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2DJH _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id P _struct_conn.ptnr1_label_comp_id 3PD _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id 3PD _struct_conn.ptnr1_auth_seq_id 117 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id O5' _struct_conn.ptnr2_label_comp_id UM3 _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id UM3 _struct_conn.ptnr2_auth_seq_id 118 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 1.595 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C10 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id 3PD _chem_comp.mon_nstd_flag . _chem_comp.name 2-AMINO-9-(2-DEOXY-3-O-PHOSPHONOPENTOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2'-DEOXYGUANOSINE-3'-MONOPHOSPHATE" # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag O5' C5' 3PD sing 1 n n O5' H5' 3PD sing 2 n n C5' C4' 3PD sing 3 n n C5' "H5'1" 3PD sing 4 n n C5' "H5'2" 3PD sing 5 n n C4' O4' 3PD sing 6 n n C4' C3' 3PD sing 7 n n C4' H4' 3PD sing 8 n n O4' C1' 3PD sing 9 n n C1' C2' 3PD sing 10 n n C1' N9 3PD sing 11 n n C1' H1' 3PD sing 12 n n C2' C3' 3PD sing 13 n n C2' "H2'1" 3PD sing 14 n n C2' "H2'2" 3PD sing 15 n n C3' O3' 3PD sing 16 n n C3' H3' 3PD sing 17 n n O3' P 3PD sing 18 n n N9 C4 3PD sing 19 n y N9 C8 3PD sing 20 n y C4 N3 3PD sing 21 n y C4 C5 3PD doub 22 n y N3 C2 3PD doub 23 n y C2 N2 3PD sing 24 n n C2 N1 3PD sing 25 n y N2 HN21 3PD sing 26 n n N2 HN22 3PD sing 27 n n N1 C6 3PD sing 28 n y N1 HN1 3PD sing 29 n n C6 O6 3PD doub 30 n n C6 C5 3PD sing 31 n y C5 N7 3PD sing 32 n y N7 C8 3PD doub 33 n y C8 H8 3PD sing 34 n n P O1P 3PD sing 35 n n P O2P 3PD sing 36 n n P O1 3PD doub 37 n n O1P H1P 3PD sing 38 n n O2P H2P 3PD sing 39 n n # _atom_sites.entry_id 2DJH _atom_sites.fract_transf_matrix[1][1] 0.034258 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020525 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.01598 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 3PD A 1 117 1 3PD GU . C 3 UM3 A 1 118 1 UM3 GU . D 4 HOH A 1 119 1 HOH TIP . D 4 HOH A 2 120 2 HOH TIP . D 4 HOH A 3 121 3 HOH TIP . D 4 HOH A 4 122 4 HOH TIP . D 4 HOH A 5 123 5 HOH TIP . D 4 HOH A 6 124 6 HOH TIP . D 4 HOH A 7 125 7 HOH TIP . D 4 HOH A 8 126 8 HOH TIP . D 4 HOH A 9 127 9 HOH TIP . D 4 HOH A 10 128 11 HOH TIP . D 4 HOH A 11 129 12 HOH TIP . D 4 HOH A 12 130 13 HOH TIP . D 4 HOH A 13 131 14 HOH TIP . D 4 HOH A 14 132 15 HOH TIP . D 4 HOH A 15 133 16 HOH TIP . D 4 HOH A 16 134 17 HOH TIP . D 4 HOH A 17 135 18 HOH TIP . D 4 HOH A 18 136 19 HOH TIP . D 4 HOH A 19 137 21 HOH TIP . D 4 HOH A 20 138 22 HOH TIP . D 4 HOH A 21 139 23 HOH TIP . D 4 HOH A 22 140 24 HOH TIP . D 4 HOH A 23 141 25 HOH TIP . D 4 HOH A 24 142 26 HOH TIP . D 4 HOH A 25 143 27 HOH TIP . D 4 HOH A 26 144 28 HOH TIP . D 4 HOH A 27 145 29 HOH TIP . D 4 HOH A 28 146 30 HOH TIP . D 4 HOH A 29 147 31 HOH TIP . D 4 HOH A 30 148 32 HOH TIP . D 4 HOH A 31 149 33 HOH TIP . D 4 HOH A 32 150 34 HOH TIP . D 4 HOH A 33 151 35 HOH TIP . D 4 HOH A 34 152 36 HOH TIP . D 4 HOH A 35 153 37 HOH TIP . D 4 HOH A 36 154 38 HOH TIP . D 4 HOH A 37 155 39 HOH TIP . D 4 HOH A 38 156 40 HOH TIP . D 4 HOH A 39 157 41 HOH TIP . D 4 HOH A 40 158 42 HOH TIP . D 4 HOH A 41 159 43 HOH TIP . D 4 HOH A 42 160 44 HOH TIP . D 4 HOH A 43 161 45 HOH TIP . D 4 HOH A 44 162 46 HOH TIP . D 4 HOH A 45 163 47 HOH TIP . D 4 HOH A 46 164 48 HOH TIP . D 4 HOH A 47 165 49 HOH TIP . D 4 HOH A 48 166 50 HOH TIP . D 4 HOH A 49 167 51 HOH TIP . D 4 HOH A 50 168 52 HOH TIP . D 4 HOH A 51 169 53 HOH TIP . D 4 HOH A 52 170 54 HOH TIP . D 4 HOH A 53 171 55 HOH TIP . D 4 HOH A 54 172 56 HOH TIP . D 4 HOH A 55 173 57 HOH TIP . D 4 HOH A 56 174 58 HOH TIP . D 4 HOH A 57 175 59 HOH TIP . D 4 HOH A 58 176 60 HOH TIP . D 4 HOH A 59 177 61 HOH TIP . D 4 HOH A 60 178 62 HOH TIP . D 4 HOH A 61 179 63 HOH TIP . D 4 HOH A 62 180 64 HOH TIP . D 4 HOH A 63 181 65 HOH TIP . D 4 HOH A 64 182 66 HOH TIP . D 4 HOH A 65 183 67 HOH TIP . D 4 HOH A 66 184 68 HOH TIP . D 4 HOH A 67 185 69 HOH TIP . D 4 HOH A 68 186 70 HOH TIP . D 4 HOH A 69 187 71 HOH TIP . D 4 HOH A 70 188 72 HOH TIP . D 4 HOH A 71 189 73 HOH TIP . D 4 HOH A 72 190 75 HOH TIP . D 4 HOH A 73 191 76 HOH TIP . D 4 HOH A 74 192 77 HOH TIP . D 4 HOH A 75 193 78 HOH TIP . D 4 HOH A 76 194 79 HOH TIP . D 4 HOH A 77 195 80 HOH TIP . D 4 HOH A 78 196 81 HOH TIP . D 4 HOH A 79 197 82 HOH TIP . D 4 HOH A 80 198 83 HOH TIP . D 4 HOH A 81 199 84 HOH TIP . D 4 HOH A 82 200 85 HOH TIP . D 4 HOH A 83 201 86 HOH TIP . D 4 HOH A 84 202 87 HOH TIP . D 4 HOH A 85 203 88 HOH TIP . D 4 HOH A 86 204 89 HOH TIP . D 4 HOH A 87 205 90 HOH TIP . D 4 HOH A 88 206 91 HOH TIP . D 4 HOH A 89 207 92 HOH TIP . D 4 HOH A 90 208 93 HOH TIP . D 4 HOH A 91 209 94 HOH TIP . D 4 HOH A 92 210 95 HOH TIP . D 4 HOH A 93 211 96 HOH TIP . D 4 HOH A 94 212 97 HOH TIP . D 4 HOH A 95 213 98 HOH TIP . D 4 HOH A 96 214 99 HOH TIP . D 4 HOH A 97 215 100 HOH TIP . D 4 HOH A 98 216 101 HOH TIP . D 4 HOH A 99 217 102 HOH TIP . D 4 HOH A 100 218 103 HOH TIP . D 4 HOH A 101 219 104 HOH TIP . D 4 HOH A 102 220 105 HOH TIP . D 4 HOH A 103 221 106 HOH TIP . D 4 HOH A 104 222 107 HOH TIP . D 4 HOH A 105 223 108 HOH TIP . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 O O5' 3PD . . . B 2 11.162 13.419 0.929 1 25.5 ? O5' 3PD 117 A 1 HETATM 2 C C5' 3PD . . . B 2 11.969 12.786 1.922 1 21.44 ? C5' 3PD 117 A 1 HETATM 3 C C4' 3PD . . . B 2 13.049 13.724 2.431 1 21.61 ? C4' 3PD 117 A 1 HETATM 4 O O4' 3PD . . . B 2 13.999 14.095 1.382 1 20.9 ? O4' 3PD 117 A 1 HETATM 5 C C1' 3PD . . . B 2 14.465 15.412 1.567 1 20.05 ? C1' 3PD 117 A 1 HETATM 6 C C2' 3PD . . . B 2 13.768 16.007 2.807 1 21.09 ? C2' 3PD 117 A 1 HETATM 7 C C3' 3PD . . . B 2 12.553 15.059 3.019 1 21.05 ? C3' 3PD 117 A 1 HETATM 8 O O3' 3PD . . . B 2 12.253 14.819 4.418 1 22.03 ? O3' 3PD 117 A 1 HETATM 9 N N9 3PD . . . B 2 14.282 16.183 0.267 1 19.95 ? N9 3PD 117 A 1 HETATM 10 C C4 3PD . . . B 2 13.104 16.516 -0.407 1 20.68 ? C4 3PD 117 A 1 HETATM 11 N N3 3PD . . . B 2 11.798 16.192 -0.006 1 18.99 ? N3 3PD 117 A 1 HETATM 12 C C2 3PD . . . B 2 10.835 16.654 -0.858 1 18.8 ? C2 3PD 117 A 1 HETATM 13 N N2 3PD . . . B 2 9.536 16.441 -0.624 1 19.05 ? N2 3PD 117 A 1 HETATM 14 N N1 3PD . . . B 2 11.153 17.382 -2.023 1 20.31 ? N1 3PD 117 A 1 HETATM 15 C C6 3PD . . . B 2 12.488 17.721 -2.453 1 20.71 ? C6 3PD 117 A 1 HETATM 16 O O6 3PD . . . B 2 12.639 18.363 -3.493 1 22.72 ? O6 3PD 117 A 1 HETATM 17 C C5 3PD . . . B 2 13.505 17.234 -1.55 1 19.96 ? C5 3PD 117 A 1 HETATM 18 N N7 3PD . . . B 2 14.885 17.352 -1.6 1 20.8 ? N7 3PD 117 A 1 HETATM 19 C C8 3PD . . . B 2 15.291 16.725 -0.523 1 18.53 ? C8 3PD 117 A 1 HETATM 20 P P 3PD . . . B 2 12.056 15.963 5.526 1 20.44 ? P 3PD 117 A 1 HETATM 21 O O1P 3PD . . . B 2 13.31 16.097 6.284 1 21.26 ? O1P 3PD 117 A 1 HETATM 22 O O2P 3PD . . . B 2 11.528 17.191 4.89 1 18.74 ? O2P 3PD 117 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #